Article
Biotechnology & Applied Microbiology
Sukhen Das Mandal, Partho Sarothi Ray
Summary: m(6)A-modified mRNAs are more targeted by miRNAs and RBPs, with miRNA target sites and RBP-binding sites located close to m(6)A sites, indicating a three-way interplay between m(6)A, microRNA, and RBP binding.
Article
Biotechnology & Applied Microbiology
Vaishnovi Sekar, Emilio Marmol-Sanchez, Panagiotis Kalogeropoulos, Laura Stanicek, Eduardo A. Sagredo, Albin Widmark, Evangelos Doukoumopoulos, Franziska Bonath, Inna Biryukova, Marc R. Friedlander
Summary: In this study, a new method called agoTRIBE is developed to comprehensively detect miRNA targets at the single-cell level. By fusing Argonaute2 protein with the RNA editing domain of ADAR2, the method allows sensitive single-cell RNA sequencing to identify miRNA targets. The results show that agoTRIBE can identify functional miRNA targets and obtain transcriptome-wide measurements of RNA abundance.
NATURE BIOTECHNOLOGY
(2023)
Article
Cell Biology
Lijie Wang, Wei Xue, Hongxia Zhang, Runze Gao, Houyuan Qiu, Jia Wei, Lina Zhou, Yun-Ni Lei, Xiaocheng Wu, Xiao Li, Chengfang Liu, Jing Wu, Qiubing Chen, Hanhui Ma, Xingxu Huang, Cheguo Cai, Ying Zhang, Bei Yang, Hao Yin, Li Yang, Jia Chen
Summary: The study introduces a novel base editor system, tBE, which efficiently performs C-to-T editing by fusing a cleavable dCDI domain, reducing off-target mutations. The tBE system remains inactive at off-target sites, preventing unintended mutations, and activates for precise base editing at on-target sites.
NATURE CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Siqian Jin, Ziwei Xue, Jinchun Zhang, Ziqi Wang, Jin Zhang, Di Chen, Wanlu Liu, Junxin Lin
Summary: This study utilized TRIBE to identify RNA targets and binding motifs of SRSF3 in human embryonic stem cells, revealing that the binding sites of SRSF3 are mainly distributed in exons and potentially conserved in mammals.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Steven M. Blue, Brian A. Yee, Gabriel A. Pratt, Jasmine R. Mueller, Samuel S. Park, Alexander A. Shishkin, Anne C. Starner, Eric L. Van Nostrand, Gene W. Yeo
Summary: The discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets is crucial for understanding the regulation of RNA processing. In this study, a method called seCLIP is presented, which allows for efficient and high-resolution analysis of these interactions, along with a comprehensive bioinformatics pipeline.
Article
Multidisciplinary Sciences
Aaron A. Smargon, Assael A. Madrigal, Brian A. Yee, Kevin D. Dong, Jasmine R. Mueller, Gene W. Yeo
Summary: This study reveals that Cas9 can interact with endogenous human RNA transcripts in human cells, and this interaction is correlated with elevated RNA editing even under guide RNA co-expression. However, there is no evidence to support the hypothesis that human RNAs can guide Cas9 to bind and cleave human genomic DNA broadly.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Sumirtha Balaratnam, Curran Rhodes, Desta Doro Bume, Colleen Connelly, Christopher C. Lai, James A. Kelley, Kamyar Yazdani, Philip J. Homan, Danny Incarnato, Tomoyuki Numata, John S. Schneekloth
Summary: This study investigates the modification ability of various PreQ(1)-derived probes on the riboswitch aptamer, revealing successful binding and retention of activity for one probe. Transcriptome-wide mapping shows highly selective interaction between the bacterial aptamer and the probe, with evidence of possible PreQ(1) aptamers in human RNA.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Chachrit Khunsriraksakul, Daniel McGuire, Renan Sauteraud, Fang Chen, Lina Yang, Lida Wang, Jordan Hughey, Scott Eckert, J. Dylan Weissenkampen, Ganesh Shenoy, Olivia Marx, Laura Carrel, Bibo Jiang, Dajiang J. Liu
Summary: Here, the authors propose an integrative method PUMICE to improve gene expression predictions by integrating 3D genomic and epigenomic data with expression quantitative trait loci (eQTL). The method outperforms other competing methods and identifies more novel genes. Additionally, an extension to the method, PUMICE +, shows improved performance in computational drug repurposing.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Ute A. Hoffmann, Florian Heyl, Said N. Rogh, Thomas Wallner, Rolf Backofen, Wolfgang R. Hess, Claudia Steglich, Annegret Wilde
Summary: Ribonucleases are essential enzymes in RNA metabolism and post-transcriptional regulation in bacteria. Cyanobacteria encode two key ribonucleases, RNase E and RNase J. The study demonstrates the significant role of RNase E in post-transcriptional regulation, with potential redundant or concerted action with RNase J in cyanobacteria.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Dong-Bei Xu, Ya-Nan Ma, Teng-Fei Qin, Wei-Lin Tang, Xi-Wu Qi, Xia Wang, Rui-Cen Liu, Hai-Ling Fang, Ze-Qun Chen, Cheng-Yuan Liang, Wei Wu
Summary: Jasmonate ZIM-domain (JAZ) proteins are crucial transcriptional repressors in the jasmonic acid (JA) signaling process, and play important roles in plant development, defense, and metabolism. The study identified seven non-redundant JAZ genes in Mentha canadensis L., showing differential expression patterns in plant tissues, preferential expression in flowers, and variable responses to MeJA, ABA, drought, and salt treatments. Subcellular localization analysis demonstrated that McJAZ proteins are localized in the nucleus or cytoplasm, and yeast two-hybrid assays showed interactions between McJAZ proteins and McCOI1a.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Veterinary Sciences
Xiaoyun Wu, Min Chu, Xiaoming Ma, Jie Pei, Lin Xiong, Xian Guo, Chunnian Liang, Ping Yan
Summary: This study presents the first genome-wide characterization of RNA editing sites in yak skeletal muscles, revealing their potential involvement in important pathways related to skeletal muscle development and myogenesis. The identification of these editing sites enhances our understanding of the mechanisms underlying skeletal muscle development.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Microbiology
Karunakaran Kalesh, Wenbin Wei, Brian S. Mantilla, Theodoros Roumeliotis, Jyoti Choudhary, Paul W. Denny
Summary: This study identified RNA-binding proteins in Leishmania, including proteins that interact with non-adenylated RNAs. The study also revealed the involvement of RNA-protein interactions in various biological processes in Leishmania, such as gene regulation and protein synthesis. Additionally, the study showed the impact of heat shock protein 90 inhibition on RNA-protein interactions in Leishmania.
MICROBIOLOGY SPECTRUM
(2022)
Article
Oncology
Varshni Rajagopal, Astrid-Solveig Loubal, Niklas Engel, Elsa Wassmer, Jeanette Seiler, Oliver Schilling, Maiwen Caudron-Herger, Sven Diederichs
Summary: In this study, we identified RNA-dependent proteins in A549 lung cancer cells, providing insights into their role in cancer. The dataset is available in the R-DeeP 2.0 database, which offers detailed information on RNA-dependent proteins in A549 and HeLa cells.
Article
Biochemical Research Methods
Lishen Zhang, Chengqian Lu, Min Zeng, Yaohang Li, Jianxin Wang
Summary: In this study, we propose a method called CRMSS for discriminating circRNA-RBP binding sites based on multi-scale characterizing sequence and structure features. The CRMSS achieves superior performance over state-of-the-art methods in predicting circRNA-RBP binding.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Chen Sisi, Deng Jieru, Cheng Peidong, Zhang Zhaolong, Wang Yihang, Chen Shuwen, Tang Yan, Wang Tianyu, Yang Guiyan
Summary: This study investigated the stress response mechanism of walnut trees by analyzing the PP2C genes in walnut trees. The results showed that JrPP2C genes exhibited diversity in response to stress and ABA treatment, indicating their potential roles in plant response to multiple stimuli and involvement in ABA-dependent signaling pathway.
Article
Immunology
Andreas Walker, Torsten Houwaart, Patrick Finzer, Lutz Ehlkes, Alona Tyshaieva, Maximilian Damagnez, Daniel Strelow, Ashley Duplessis, Jessica Nicolai, Tobias Wienemann, Teresa Tamayo, Malte Kohns Vasconcelos, Lisanna Huelse, Katrin Hoffmann, Nadine Luebke, Sandra Hauka, Marcel Andree, Martin P. Daeumer, Alexander Thielen, Susanne Kolbe-Busch, Klaus Goebels, Rainer Zotz, Klaus Pfeffer, Joerg Timm, Alexander T. Dilthey
Summary: Tracing SARS-CoV-2 population transmission chains remains a major challenge, but this study presents an integrated system of genomic surveillance that is capable of detecting infection chains in a large city during ongoing community transmission. The system combines viral surveillance sequencing, genetically based identification of infection clusters, integration of public health authority contact tracing data, and a user-friendly dashboard application. This integrated system can contribute to the monitoring and potentially improve the management of SARS-CoV-2 transmission in the population.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Immunology
Jue Feng, Joseph N. Pucella, Geunhyo Jang, Marcela Alcantara-Hernandez, Samik Upadhaya, Nicholas M. Adams, Alireza Khodadadi-Jamayran, Colleen M. Lau, Marlon Stoeckius, Stephanie Hao, Peter Smibert, Aristotelis Tsirigos, Juliana Idoyaga, Boris Reizis
Summary: This study investigates the developmental origins of dendritic cells (DCs) and reveals the shared origin of pDCs and cDCs, suggesting a revised scheme of DC development.
Article
Multidisciplinary Sciences
Ulrike Zinnall, Miha Milek, Igor Minia, Carlos H. Vieira-Vieira, Simon Mueller, Guido Mastrobuoni, Orsalia-Georgia Hazapis, Simone Del Giudice, David Schwefel, Nadine Bley, Franka Voigt, Jeffrey A. Chao, Stefan Kempa, Stefan Huettelmaier, Matthias Selbach, Markus Landthaler
Summary: HDLBP/Vigilin directly interacts with more than 80% of ER-localized mRNAs and plays an important role in the translation of ER-targeted mRNAs. Its absence leads to impaired protein synthesis and secretion, as well as decreased tumor growth.
NATURE COMMUNICATIONS
(2022)
Article
Neurosciences
Andreia Gomes-Duarte, Morten T. Veno, Marina de Wit, Ketharini Senthilkumar, Mark H. Broekhoven, Joelle van den Herik, Fleur R. Heeres, Danielle van Rossum, Mateja Rybiczka-Tesulov, Ivano Legnini, Peter C. van Rijen, Pieter van Eijsden, Peter H. Gosselaar, Nikolaus Rajewsky, Jorgen Kjems, Vamshidhar R. Vangoor, R. Jeroen Pasterkamp
Summary: This study identifies differentially expressed circRNAs in the hippocampus and cortex of patients with mesial temporal lobe epilepsy (mTLE). It reveals that circ_Satb1, derived from SATB1, is decreased in mTLE patients and experimental epilepsy. Knockdown of circ_Satb1 leads to defects in dendritic spine morphology, providing new insights into the pathogenesis of mTLE.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Cardiac & Cardiovascular Systems
Ellen G. Avery, Hendrik Bartolomaeus, Ariana Rauch, Chia-Yu Chen, Gabriele N'Diaye, Ulrike Loeber, Theda U. P. Bartolomaeus, Raphaela Fritsche-Guenther, Andre F. Rodrigues, Alex Yarritu, Cheng Zhong, Lingyan Fei, Dmitry Tsvetkov, Mihail Todiras, Joon-Keun Park, Lajos Marko, Andras Maifeld, Andreas Patzak, Michael Bader, Stefan Kempa, Jennifer A. Kirwan, Sofia K. Forslund, Dominik N. Mueller, Nicola Wilck
Summary: This study investigated the impact of microbial colonization on organ damage in hypertension using germ-free and colonized mice models. The results showed that the kidney is more sensitive to microbial influence, and the colonization status is associated with circulating metabolites and inflammatory cells relevant to hypertension.
CARDIOVASCULAR RESEARCH
(2023)
Article
Urology & Nephrology
Karen Lopez-Cayuqueo, Rosa Planells-Cases, Matthias Pietzke, Anna Oliveras, Stefan Kempa, Sebastian Bachmann, Thomas J. Jentsch
Summary: The study found that all five VRAC subunits are expressed in the kidney with distinct localizations. LRRC8C is mainly found in vascular endothelial cells, LRRC8E is specific to intercalated cells, while LRRC8A, LRRC8B, and LRRC8D are prominent in the basolateral membranes of proximal tubules. Conditional deletion of LRRC8A in proximal tubules results in injury and symptoms.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Safak Bayram, Yasmin Sophiya Razzaque, Sabrina Geisberger, Matthias Pietzke, Susanne Fuerst, Carolina Vechiatto, Martin Forbes, Guido Mastrobuoni, Stefan Kempa
Summary: Cellular glutamine synthesis plays a crucial role in protecting cells from nutrient deprivation and drug resistance. By using targeted stable isotope resolved metabolomics, this study directly measured the activity of glutamine synthetase and traced the fate of glutamine derived nitrogen in the cells' biochemical network. The results highlight the importance of glutamine synthetase in overcoming glutamine depletion and the potential of dual-isotope tracing methods in medical research.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Urology & Nephrology
Johannes Holle, Hendrik Bartolomaeus, Ulrike Loeber, Felix Behrens, Theda U. P. Bartolomaeus, Harithaa Anandakumar, Moritz I. I. Wimmer, Dai Long Vu, Mathias Kuhring, Ulrike Bruening, Andras Maifeld, Sabrina Geisberger, Stefan Kempa, Fabian Schumacher, Burkhard Kleuser, Philip Bufler, Uwe Querfeld, Stefanie Kitschke, Denise Engler, Leonard D. D. Kuhrt, Oliver Drechsel, Kai-Uwe Eckardt, Sofia K. K. Forslund, Andrea Thuermer, Victoria McParland, Jennifer A. A. Kirwan, Nicola Wilck, Dominik Mueller
Summary: Patients with chronic kidney disease (CKD) exhibit a proinflammatory immune response, potentially associated with gut dysbiosis, leading to gut barrier dysfunction and microbial metabolite imbalance, which significantly influences susceptibility to cardiovascular disease.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Nir Ben-Chetrit, Xiang Niu, Ariel D. D. Swett, Jesus Sotelo, Maria S. S. Jiao, Caitlin M. M. Stewart, Catherine Potenski, Paulius Mielinis, Patrick Roelli, Marlon Stoeckius, Dan A. A. Landau
Summary: Spatial transcriptomics and proteomics have independently revolutionized our understanding of complex biological processes by providing complementary information. However, integrating these modalities in experiments has been limited. To address this, we developed Spatial PrOtein and Transcriptome Sequencing (SPOTS) for simultaneous high-throughput spatial transcriptomics and protein profiling. SPOTS significantly improves signal resolution, cell clustering, and enhances the discovery power for differential gene expression analysis across tissue regions compared to unimodal measurements.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tobias Opialla, Benjamin Gollasch, Peter H. J. L. Kuich, Lars Klug, Gabriele Rahn, Andreas Busjahn, Simone Spuler, Michael Boschmann, Jennifer A. Kirwan, Friedrich C. Luft, Stefan Kempa
Summary: The study developed a blood-drop method to assess metabolism in exercising individuals. The findings suggest that glucose availability and oxidative capacity play important roles in confronting maximal exertion.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Cell Biology
Beatriz F. Corte-Real, Ibrahim Hamad, Rebeca Arroyo Hornero, Sabrina Geisberger, Joris Roels, Lauren Van Zeebroeck, Aleksandra Dyczko, Marike W. van Gisbergen, Henry Kurniawan, Allon Wagner, Nir Yoset, Susanne N. Y. Weiss, Klaus G. Schmetterer, Agnes Schroeder, Luka Krampert, Stefanie Haase, Hendrik Bartolomaeus, Niels Hellings, Yvan Saeys, Ludwig J. Dubois, Dirk Brenner, Stefan Kempa, David A. Hafler, Johannes Stegbauer, Ralf A. Linker, Jonathan Jantsch, Dominik N. Mueller, Markus Kleinewietfeld
Summary: High salt induces metabolic reprogramming in human Tregs, leading to pro-inflammatory features and FOXP3 downregulation, which has important implications for autoimmunity.
Correction
Biochemistry & Molecular Biology
Tobias Opialla, Benjamin Gollasch, Peter H. J. L. Kuich, Lars Klug, Gabriele Rahn, Andreas Busjahn, Simone Spuler, Michael Boschmann, Jennifer A. Kirwan, Friedrich C. Luft, Stefan Kempa
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biology
Julia Loeffler, Anne Noom, Agnes Ellinghaus, Anke Dienelt, Stefan Kempa, Georg N. Duda
Summary: Bone regeneration after fracture is a complex process with high and dynamic energy demands. Metabolites, particularly succinate, are shown to play central roles as signaling molecules during the onset of healing and in steering bone tissue regeneration. Succinate is found to promote vascularization and ossification, highlighting that metabolites have the potential to be used therapeutically to promote fracture healing.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Ivano Legnini, Lisa Emmenegger, Alessandra Zappulo, Agnieszka Rybak-Wolf, Ricardo Wurmus, Anna Oliveras Martinez, Cledi Cerda Jara, Anastasiya Boltengagen, Tale Hessler, Guido Mastrobuoni, Stefan Kempa, Robert Zinzen, Andrew Woehler, Nikolaus Rajewsky
Summary: This study combines optogenetics and gene perturbation technologies to activate or knock down target genes in organoids with programmable spatiotemporal patterns. The research shows that local activation of specific signaling pathways is sufficient to generate organoids with stereotypical patterns and provides new insights into gene regulation in neurodevelopment. Thus, optogenetic perturbations in combination with spatial transcriptomics is a powerful technology for reprogramming and studying cell fates and tissue patterning in organoids.